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Chapter 17 : Molecular Biology of the Model Piezophile, DSS12

Authors: Chiaki Kato1, Takako Sato2, Kaoru Nakasone3, Hideyuki Tamegai4
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Affiliations: 1: Extremobiosphere Research Center, Japan Agency for Marine-Earth Science and Technology, Yokosuka 237-0061, Japan; 2: Extremobiosphere Research Center, Japan Agency for Marine-Earth Science and Technology, Yokosuka 237-0061, Japan; 3: Department of Chemistry and Environmental Technology, School of Engineering, Kinki University, Higashi-Hiroshima 739-2116, Japan; 4: Department of Chemistry, College of Humanities and Sciences, Nihon University, Setagaya-ku, Tokyo 156-8550, Japan
Content Type: Monograph
Publication Year: 2008

Category: Applied and Industrial Microbiology

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Abstract:

This chapter focuses on the molecular characteristics of pressure adaptation in DSS12 and recent advances in developing genetics and utilizing genomics. Sigma 54 plays an important role in pressure-regulated transcription in , although it should be noted that the expression of sigma 54 is not itself regulated by pressure. Any of these trans-acting factors (sigma 54, NtrC, or NtrB) could play an important role in pressure-regulated transcription in this piezophilic bacterium. Downstream from the pressure-regulated operon described is an open reading frame (ORF) homologous to the cydD gene of . Another aspect of transcription in piezophiles is the stability of the quaternary structure of RNA polymerase. It is likely that the sigma subunit stabilizes the core enzyme through alteration of the quaternary structure of RNA polymerase, resulting in piezotolerance. One possible explanation for the low conjugation frequency is that the optimal mating temperature for DSS12R is 20°C, which is much lower than the optimal temperature for . This study provided the first demonstration of gene transfer in the piezophilic bacterium DSS12. The study of the mechanisms for adaptation to high-pressure environments, including gene regulatory systems, may now also proceed in vivo using genetic approaches in this piezophile. Therefore, genomic analysis of marine extremophiles may lead to the discovery of new functions for genes.

Citation: Kato C, Sato T, Nakasone K, Tamegai H. 2008. Molecular Biology of the Model Piezophile, DSS12, p 305-317. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch17

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Gene Expression and Regulation
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Transcription Start Site
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RNA Polymerase
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Bacterial Proteins
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Molecular Biology of the Model Piezophile, Shewanella violacea DSS12
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Citation: Kato C, Sato T, Nakasone K, Tamegai H. 2008. Molecular Biology of the Model Piezophile, DSS12, p 305-317. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch17
/content/10.1128/9781555815646.ch17.ch17fig01
Figure 1.
Diagrammatic representation of the pressure-regulated genes in strain DSS12. (A) Pressure-regulated operon; (B) glutamine synthetase operon. Bold numbers (#2 in panel A and #1 in panel B) show the transcription start sites controlled by the sigma 54 factor.
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Image of Figure 1.
Figure 1.

Diagrammatic representation of the pressure-regulated genes in strain DSS12. (A) Pressure-regulated operon; (B) glutamine synthetase operon. Bold numbers (#2 in panel A and #1 in panel B) show the transcription start sites controlled by the sigma 54 factor.

Citation: Kato C, Sato T, Nakasone K, Tamegai H. 2008. Molecular Biology of the Model Piezophile, DSS12, p 305-317. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch17
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Figure 2.
Autophosphorylation of the NtrB protein, -phosphorylation of NtrB-P to the NtrC protein in vitro, and Western blot analysis of expression of the NtrC under different pressure conditions. (A) Autophosphorylation of NtrB incubated in the presence of [γ-P]ATP at several temperature conditions. Lane 1, 0°C; lane 2, 10°C; lane 3, 24°C; lane 4, 37°C. (B) -Phosphorylation to NtrC incubated with the phosphorylated NtrB-P at 10°C for 1 min. Lane 5, phosphorylated NtrB; lane 6, phosphorylated NtrC. (C) Lysates prepared from cells cultured at 0.1 or 50 MPa were fractionated by SDS–10% PAGE and then blotted onto a polyvinylidene fluoride membrane. The membrane was treated with antiserum against NtrC.
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Image of Figure 2.
Figure 2.

Autophosphorylation of the NtrB protein, -phosphorylation of NtrB-P to the NtrC protein in vitro, and Western blot analysis of expression of the NtrC under different pressure conditions. (A) Autophosphorylation of NtrB incubated in the presence of [γ-P]ATP at several temperature conditions. Lane 1, 0°C; lane 2, 10°C; lane 3, 24°C; lane 4, 37°C. (B) -Phosphorylation to NtrC incubated with the phosphorylated NtrB-P at 10°C for 1 min. Lane 5, phosphorylated NtrB; lane 6, phosphorylated NtrC. (C) Lysates prepared from cells cultured at 0.1 or 50 MPa were fractionated by SDS–10% PAGE and then blotted onto a polyvinylidene fluoride membrane. The membrane was treated with antiserum against NtrC.

Citation: Kato C, Sato T, Nakasone K, Tamegai H. 2008. Molecular Biology of the Model Piezophile, DSS12, p 305-317. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch17
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Figure 3.
Model for pressure regulation of gene expression in the piezophilic strain DSS12.
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Image of Figure 3.
Figure 3.

Model for pressure regulation of gene expression in the piezophilic strain DSS12.

Citation: Kato C, Sato T, Nakasone K, Tamegai H. 2008. Molecular Biology of the Model Piezophile, DSS12, p 305-317. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch17
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Figure 4.
Reduced minus oxidized difference spectra of membrane fractions from Each fraction was obtained from the cells grown under a pressure of 0.1 MPa with shaking (A), grown under a pressure of 0.1 MPa under microaerobic conditions (B), and grown under a pressure of 50 MPa with microaerobic conditions (C). An absorption peak at 629 nm and a trough at 649 nm are specifically detected in the membrane fraction of cells grown under a pressure of 50 MPa. These spectral properties are typical of -type cytochromes ( ).
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Image of Figure 4.
Figure 4.

Reduced minus oxidized difference spectra of membrane fractions from Each fraction was obtained from the cells grown under a pressure of 0.1 MPa with shaking (A), grown under a pressure of 0.1 MPa under microaerobic conditions (B), and grown under a pressure of 50 MPa with microaerobic conditions (C). An absorption peak at 629 nm and a trough at 649 nm are specifically detected in the membrane fraction of cells grown under a pressure of 50 MPa. These spectral properties are typical of -type cytochromes ( ).

Citation: Kato C, Sato T, Nakasone K, Tamegai H. 2008. Molecular Biology of the Model Piezophile, DSS12, p 305-317. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch17
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Figure 5.
Diagram of the HPEA. (A) High-pressure electrophoresis chamber for HPEA.(a) Connection to the power supply (anode); (b) connection to the power supply (cathode); (c) buffers; (d) silicone oil KF-96-1.5CS; (e) glass microcapillary tube; (f) O-ring to partition a space into the upper and lower spaces; (g) connection to a high-pressure pump. (B) Photograph of the HPEA. 1, high-pressure electrophoresis chamber; 2, high-pressure hand pump; 3, pressure gauge.
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10.1128/9781555815646/f0311-01.gif
Image of Figure 5.
Figure 5.

Diagram of the HPEA. (A) High-pressure electrophoresis chamber for HPEA.(a) Connection to the power supply (anode); (b) connection to the power supply (cathode); (c) buffers; (d) silicone oil KF-96-1.5CS; (e) glass microcapillary tube; (f) O-ring to partition a space into the upper and lower spaces; (g) connection to a high-pressure pump. (B) Photograph of the HPEA. 1, high-pressure electrophoresis chamber; 2, high-pressure hand pump; 3, pressure gauge.

Citation: Kato C, Sato T, Nakasone K, Tamegai H. 2008. Molecular Biology of the Model Piezophile, DSS12, p 305-317. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch17
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Figure 6.
Effects of high hydrostatic pressure on subunit association in RNA polymerase in (A), (B), and without sigma factor (C). Native PAGE was performed at 0.1 MPa (upper panels) or 140 MPa (lower panels), followed by SDS-PAGE at 0.1 MPa. Proteins were visualized by silver staining. Each subunit of RNA polymerase is shown by an open circle. M, molecular mass markers; 1st dim, one-dimensional separation; 2nd dim, two-dimensional separation.
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10.1128/9781555815646/f0312-01.gif
Image of Figure 6.
Figure 6.

Effects of high hydrostatic pressure on subunit association in RNA polymerase in (A), (B), and without sigma factor (C). Native PAGE was performed at 0.1 MPa (upper panels) or 140 MPa (lower panels), followed by SDS-PAGE at 0.1 MPa. Proteins were visualized by silver staining. Each subunit of RNA polymerase is shown by an open circle. M, molecular mass markers; 1st dim, one-dimensional separation; 2nd dim, two-dimensional separation.

Citation: Kato C, Sato T, Nakasone K, Tamegai H. 2008. Molecular Biology of the Model Piezophile, DSS12, p 305-317. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch17
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Figure 7.
Images of 1% agarose electrophoresis of plasmid extracted from DSS12R transconjugants.
10.1128/9781555815646/f0314-01_thmb.gif
10.1128/9781555815646/f0314-01.gif
Image of Figure 7.
Figure 7.

Images of 1% agarose electrophoresis of plasmid extracted from DSS12R transconjugants.

Citation: Kato C, Sato T, Nakasone K, Tamegai H. 2008. Molecular Biology of the Model Piezophile, DSS12, p 305-317. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch17
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Figure 8.
Annotation of ORFs in the genome. The total genome size is 4.9 Mbp, and approximately 4,600 ORFs are predicted.
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10.1128/9781555815646/f0314-02.gif
Image of Figure 8.
Figure 8.

Annotation of ORFs in the genome. The total genome size is 4.9 Mbp, and approximately 4,600 ORFs are predicted.

Citation: Kato C, Sato T, Nakasone K, Tamegai H. 2008. Molecular Biology of the Model Piezophile, DSS12, p 305-317. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch17
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References

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Tables

Molecular Biology of the Model Piezophile, Shewanella violacea DSS12
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Citation: Kato C, Sato T, Nakasone K, Tamegai H. 2008. Molecular Biology of the Model Piezophile, DSS12, p 305-317. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch17
/content/10.1128/9781555815646.ch17.ch17tab01
TABLE 1.
Composition of cytochromes in
Generic image for table
TABLE 1.

Composition of cytochromes in

Citation: Kato C, Sato T, Nakasone K, Tamegai H. 2008. Molecular Biology of the Model Piezophile, DSS12, p 305-317. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch17
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TABLE 2.
Comparison of DSS12 conjugation efficiencies with different plasmids
Generic image for table
TABLE 2.

Comparison of DSS12 conjugation efficiencies with different plasmids

Citation: Kato C, Sato T, Nakasone K, Tamegai H. 2008. Molecular Biology of the Model Piezophile, DSS12, p 305-317. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch17

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